Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.62 kDa 
• Atom Count: 1,933 
• Modelled Residue Count: 222 
• Deposited Residue Count: 230 
• Unique protein chains: 2

 4LKL

Crystal structure of Plk1 Polo-box domain in complex with PL-55

• PDB DOI:  https://doi.org/10.2210/pdb4LKL/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-08 Released: 2013-12-11 
• Deposition Author(s): Lee, W.C., Song, J.H., Kim, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 

Literature

Exploring the binding nature of pyrrolidine pocket-dependent interactions in the polo-box domain of polo-like kinase 1

Murugan, R.N., Ahn, M., Lee, W.C., Kim, H.Y., Song, J.H., Cheong, C., Hwang, E., Seo, J.H., Shin, S.Y., Choi, S.H., Park, J.E., Bang, J.K.

(2013) PLoS One 8: e80043-e80043

• PubMed: 24223211 
• DOI: https://doi.org/10.1371/journal.pone.0080043
• Primary Citation of Related Structures:  
  4LKL, 4LKM


• PubMed Abstract: 
  

Over the years, a great deal of effort has been focused on the design and synthesis of potent, linear peptide inhibitors targeting the polo-like kinase 1 (Plk1), which is critically involved in multiple mitotic processes and has been established as an adverse prognostic marker for tumor patients. Plk1 localizes to its intracellular anchoring sites via its polo-box domain, and inhibiting the Plk1 polo-box domain has been considered as an approach to circumvent the specificity problems associated with inhibiting the conserved adenosine triphosphate-binding pocket. The polo-box domain consists of two different binding regions, such as the unique, broader pyrrolidine-binding pocket and the conserved, narrow, Tyr-rich hydrophobic channel, among the three Plk polo-box domains (Plks 1-3), respectively. Therefore, the studies that provide insights into the binding nature of the unique, broader pyrrolidine-binding pocket might lead to the development of selective Plk1-inhibitory compounds.

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Organizational Affiliation: 

Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	222	Homo sapiens	Mutation(s): 0  Gene Names: PLK1, PLK EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens) Explore P53350  Go to UniProtKB:  P53350
PHAROS:  P53350

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PL-55	B	8	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADM	C [auth B]	ADAMANTANE C10 H16 ORILYTVJVMAKLC-YNFQOJQRSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001156	B	PL-55	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.34	α = 90
b = 50.94	β = 97.61
c = 57	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Lee, W.C., Song, J.H., Kim, H.Y.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release